mmg_233_2013_genetics_genomicswikiaorg-20200214-history
Streptococcus: Replacing and Additive Horizontal Gene Transfer
Introduction Streptococcus ''is a genus of spherical gram-positive bacteria belonging to the phlum Firmicutes and the lactic acid bacteria group (1) . Previously thought to be a superfamily containing over 50 species have since been separated into genera ''Enterococcus ''and ''Lactococcus (1). The Strep. family consists of many members divided into three sections: alpha-hemolytic, beta-hemolytic and gamma-hemolytic. Many of the Strep. family members are actually non-pathogenic and have definitive roles within the human microbiome of the mouth, skin, GI tract and upper respitory tract. Although, there are pathogenic forms that have deleterious effects on humans, such as pink eye, strep throat, bacterial pneumonia, endocarditis, erysipelas and necrotizing fasciitis (flesh eating bacteria) (1) (2). Horizontal Gene Transfer and Its Extensive History with Streptococcus Horizontal gene transfer (HGT) refers to a transfer of genes or genetic information between organisms outside of their normal reproduction or replication (3). HGT has played an ever increasing role in the bioevolution of bacteria, viruses, bacteriophages and plasmids. A simplified example of this would be the transfer of an antibiotic resistance gene to a bacteria such that it may grow in the presence of a given antibiotic. There are considered to be four main mechanisms that determine the mode of action: transformation, transduction, bacterial conjugation and gene transfer agents (3). For this process to occur in bacteria, two major ways define this phenomenon: the new sequence replaces a homologous sequence through the process of homologous recombination or its acquired via an additive or non-replacing integration process (4) . HGT is thought to be the primary reason for the large family of Strep and significantly contributes to its pathogenesis or lack thereof. Many of the Strep. species are concentrated in the beta-hemolytic branch pyogenic division and have adapted extensively to form a diverse set of ecological niches (2). Several studies have focused on the HGT between the human infecting SPY (Streptococcus pyogenes) and SDE (Streptococcus dysgalactiae equisimilis). SPY has long been considered pathogenic, and it wasn't till recently reported that SDE also has a pathogenic role (5). The same group inferred homology of virulence genes between SPY and SDE most likely enabled by their environmental niche and close evolutionary relationship. Although, recently, the direction of gene flow and mode of gene transfer has been a topic of question. Most of the HGT studies in Strep. have focused on based on relatively simple phylogenetic methods that infer differences in gene trees across loci. There are inherent specificity issues present with these simpler, classical methods. Often the direction of gene flow is lost and data is limited. Gene Transfer by Replacing or Adding? Armed with a complete genome sequence of SPY, SDE and related SDD (S. dysgalactiae ssp. dysgalactiae), Choi et al., were able to approach HGT in a different manner than previously accomplished. Using new statistical and parsimony-based methods for analysis, the group was able to examine both additive and replacing HGTs and compare their genome wide effects (2). Replacing HGT refers to the genes in one lineage being replaced by another while additive HGT refers to the garnering of new genetic material from a host or donor. Choi et al., found that the gene flow significantly favored the SPY-SDE direction and that the rate of replacing gene transfer far outweighed the additive gene transfer mechanism (2). This suggests that they may have been driven by homologous recombination events. In the case of SDE-SDD, the data suggested that the events may have been more additive HGT. One interesting bit of information that the group took away from the study, was that putative virulence genes are significantly associated with additive HGT but not replacing HGT. When comparing the two differing events, replacing vs additive, its important to note the events that occur are most likely to be correlated with the core and dispensable portions of the genome. Truly additive transfer events will most likely occur in the dispensable genome and recombination events occurring in the core portions. The authors do cite that further characterization will be required, although, it is important to understand that as sequence data becomes more readily available, more detailed examination of HGT can provide useful information of how the organism mutates or alters its genome. This could prove to be useful in understanding mechanics of otherwise unknown species. References #http://en.wikipedia.org/wiki/Streptococcus #Choi SC, et al. (2012) Replacing and additive horizontal gene transfer in Streptococcus. Mol Biol Evol 29(11):3309-3320. #http://en.wikipedia.org/wiki/Horizontal_gene_transfer #Thomas CM & Nielsen KM (2005) Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 3(9):711-721. #Brandt CM & Spellerberg B (2009) Human infections due to Streptococcus dysgalactiae subspecies equisimilis. Clin Infect Dis 49(5):766-772.